The Second Rise of the God Emperor of Mankind
by gondor20
Summary: The Galaxy is in ruins. The Emperor finds a way to change the future. He travels back in time to his childhood. Warhammer 40k/ Naruto Crossover.
1. Chapter 1

**Welcome to my latest story. This is going to be worked on along with 'The sleeping Dragon and the Hidden Leaf'. This is a Naruto/Warhammer 40k crossover that is going to be very different then all the other I have seen on this site. Naruto will not join Chaos. I like the evil forces of Chaos, but that idea is overdone. I have a few ideas of pairings, but I will see what people say in the reviews. Read and review! Oh, and make sure you review! Have fun.**

"Talking"

'Thinking'

**"Demon Speaking"**

**'Demon thinking'**

/ / / / / / Start of story

Prologue: The Broken Galaxy

The Emperor of Mankind looked out over Terra. The once great city was now ruins. A large fleet of Chaos ships had attacked the city and most of it was destroyed. After a long battle, the Chaos fleet had withdrawn. The Emperor sighed and turned away from his window. It has been over thirty years since he had awoken from his sleep on the golden throne. He was surprised when he saw how much the Imperium changed from when he ascended the Golden Throne. He rembered when the High Lords of Terra saw him.

/ / / / Flashback

The Emperor of Mankind walked away from his private room. He was wearing deep orange robes. Two members of the Adeptus Custodes, the Imperial Palce's Guards, stood on either side of him. It had been three weeks since he woke up. During the three weeks, he read up on current events, rested, and ate. He laughed at the faces of his guards when he asked for broth and noodles. While his guards got him his meal, he read about what has happened since he had been on the throne. A large frown formed and grew as he read about what has happened. From what he could tell, there were three major issues that the Imperium faced. The first is the Hive Fleets of the Tyranids. These strange aliens were a threat that had been pushed off for too long. He would have to assemble a fleet to take out the threat. The second issue is the Imperium itself. He looked at many of the Hive Worlds and was sick. How could the High Lords of Terra let things get so bad? The poor lived on the street and starved! The first thing the High Lords of Terra should have done was feed the people. The way to fix this was replacing some people. The third issue was the forces of Chaos. He had no doubt that they would try something, once he revealed himself.

The Emperor shook his head when he reached the two large doors that led into the meeting room of the High Lords of Terra. This was it. He cleared his mind and pushed open the door. The High Lords of Terra were talking about new shipping ideas and maybe a rise in taxes. The moment he entered the room was silent. He looked at each of the High Lords. The first one to speak was a short fat man with a fat bald head.

"I don't know who you are, but you have no right to bust in here! This is a meeting of the Great High Lords of Mankind! Leave now or I will have the guards kill you!" The Emperor just frowned. He nodded his head towards one of his guard. The guard stepped forward and grabbed the fat man and forced him to his knees.

"Kneel before the Emperor of Mankind," the guard yelled. The rest of the High Lords of Terra eyes narrowed.

"What heresy! The Emperor of Mankind is on the golden throne! Guards," a tall man with dark skin said. He wore a simple yellow coat. He had a golden 'I' with a skull on it hanging around his neck. The Emperor released some of his physic energy. Everyone in the room was filled with a strange calm. The Emperor now had a golden halo around his head.

"High Lords of Terra! I have of course made mistakes in my life, but allowing you fools to take power is my biggest mistake! From this point on I am disbanding the High Lords of Terra!" He turned his head towards the dark skinned man. "You are to come with me. I have new orders for the Inquisition!"

/ / / / / End of Flashback

The Emperor turned around and walked back into the palace. A woman was standing at the door way. She had long dark red hair and two pointed ears. She was Caluthien, an elder farseer. She smiled gently when she saw his grim face. "It is not your fault." The Emperor walked past her.

"Yes it is! If I had not been wounded by Horus, none of this would have happened! Chaos would have not burn the galaxy; the High Lords of Terra would have not been able to starve people! Untold lives would have not been lost," the Emperor yelled with a few tears coming from his eyes. Caluthien walked over and stood in front of him.

"It is not your fault. You did not cause Horus to fall. You did not lead the High Lords of Terra! While many have been lost, the rest have been spared the horrors of Chaos taking over! You did the best you could, and it was more then anyone could expect! You did something that I and many others thought impossible. You united the Eldar, The Imperium and the Tau under one banner to combat Chaos," the Eldar yelled. "While many have been lost, many have been saved."

The Emperor was silent for a few moments. "Thank you. I did do my best. Anyways, any word from the Tau fleet? Did they reach Tau?"

Caluthien sighed. "The Planet Tau is scared now. It will take a very long time for anyone to live on it again. Most of the other Tau worlds are bad. The Tau fleet is heading back to Mars."

"I see. You may go now. I want to be alone for a little bit." Caluthien nodded and left. The Emperor walked into his private room and opened a chest that was at the foot of his bed. He pulled out a picture and a torn black head band. The picture, while washed out, showed four people. The first person is an older man with long white spiky hair. He had a red outfit on. A blond woman with a VERY large rack stood next to the man. A shorter woman with black hair was holding a pig stood next to the blond. The last person was a boy with short blond hair. He had an orange jumpsuit on and a large smile on his face. _"I was so young. I miss pervy sage and baa-chan,"_ the Emperor thought. He sat the picture done and looked at the head band. You could barley see a leaf on it. _'This thing brings back memories." _ The Emperor sat the things back into the chest. He lies on his bed and fell asleep.

/ / / / / Next Morning

The Emperor walked into a large room with a bowel of oats in his hand. He saw Caluthien and a few other Eldar sitting in a corner talking. He looked over and saw a large group of Space Marine Chapter Masters talking. He sighed and sat down at the table. No one even looked at him. The Emperor sighed and started to his bowel with the spoon he was using. Everyone turned and bowed and sat down. "Thank you for all coming. We are here to talk about what is left of the orks. Now, I had the Ultramarines look for them. Can you tell us your findings?"

As the meeting was going on the Emperor was thinking. _"What if I could change this? Make every thing right. Go back in time. I wonder." _The Emperor was thinking throughout the meeting on how to change things. After the meeting, the Emperor went back to his room to think of his new plan.

Around noon Terra time, he heard a knock at the door. "Come in." Caluthien walked in with a plate of food.

"I brought you some lunch. What are you working on," The Eldar asked when she saw some of the papers on the desk he was working on.

"Thanks for the food. As for what I'm working on . . . do you believe in time travel?"

"Time Travel?"

"What if I could change every thing? Make things right. I think I may be able to been space, time, and the warp to send me back in time to prevent what has happen."

"Are you ok? This sounds crazy."

"I'm fine! I think I may be able to do this!"

"Ok let's say it is possible. How would you do it?"

"I would use my physic energy and a very old art called sealing. Using this, I will bend space and time, and send myself back! I maybe able to send some things back with me, but I'm not sure."

"Are you really ok? This is sounding really crazy."

"Whatever! I got work to do!" The Emperor turned to the papers and worked some more. Caluthien just shrugged and left.

/ / / / / / / / Two Days Later

The Emperor was finishing some of the seals needed for his idea. He had put some of his needed things in sealing scrolls and placed the scrolls on seals connected to the one he would use. When he active that seal, the others would active too. _"Done! I hope this works." _The Emperor sat in the middle of the circle and was going through the hand signs. After an hour of hand signs he was done. Nothing happened. "Damn it! I though-" the Emperor was cut off has he felt pain. He soon blacked out.

/ / / / / / ?

The Emperor opened his eyes and saw a wooden ceiling. He groaned and looked out the window and saw four stone faces. The faces of the Hokage!

"It worked," he yelled and jumped around in victory. He stopped and saw he was in his apartment from when he was a child. "I sent myself a little bit to back." He saw on the floor next to him was the scrolls he had sent back. He grabbed the first one and saw it was his power sword. The Emperor sealed the sword back and walked to his kitchen to find his calendar and ramen. After hitting some ramen up, he saw the date on the calendar. It was the day of the bell test! _"Watch out Kakashi. Naruto, the Emperor of Mankind, is going to kick your ass!"_

**DONE! This is going to be my own response to my first challenge (on my profile). This is going to be AU for both Warhammer 40k and Naruto. Naruto will be God-Like. He still has his powers from the future! As for pairings, leave me some. I was thinking maybe Kurenai or Caluthien (I will make it work). **


	2. Chapter 2

**WOW! An update so soon? Yep! I am on a role here! This chapter may or may not be as long as the previous, but this still will be good none the less. As for pairings. . . I will have a poll! Who should the God Emperor of Mankind is paired with? Who do you get to chose from? Read the list below!**

**Kurenai**

**Caluthien- She is the Eldar farseer **

**Yugito**

**Shizune**

**Hana- Kiba's Sister**

**Sister of Battle OC**

**A female Inquisitor OC- That would be funny**

**That is the list. If someone you like was not put on the list, I'm sorry. But if you PM me the person, I will add that person for an idea for a one-shot some time later! The end will be the end of wave! So vote now!**

**Oh and Disclaimer brought to you by: De Orkz**

**Da boy Gondor20 does notz ownz anyz of da thingies you may read in da story. Naruto and Warhammer 40k belongs to some weak boyz!**

**Note: If you want someone to do the disclaimer next time, leave in the reviews! **

Chapter One: A fox, a pair of bells, and an Old Man!

Naruto look at his clock. He still had two hours until Kakashi showed up. He sighed and just sat at his table in his small kitchen. _'UGH! I got to find something to do! Let's see what I can do. Summon a Warp Storm to engulf Konoha? No. Eat more Ramen? Good idea, but no. Confront Sarutobi about my parents? Maybe later. Banish the Kyuubi to the warp? I would have done it sooner or later! Why not now!' _Naruto thought to himself. Naruto sat in the middle of his living room and thought of his mindscape.

/ / / / / Mindscape

Naruto opened his eyes and saw he was in the sewer that was his mindscape. He looked up and saw two red eyes looking at him. Naruto looked up at the seal.

**"I see my jailer has come to me. What is it that you want," **the kyuubi asked as it looked at the small human in front of it. Naruto just kept looking at the seal. **"I asked you a question mortal! I AM THE KYUUBI AND YOU WILL ANSWER ME WHEN I ASK YOU SOMETHING!"**

"Blow it out your ass. I do not listen to such weak demons. I have fought humans stronger then you. As for what I want? Well, I'm going to send you back to the warp of course!"

**"MORTAL! I AM THE GREAT KYUUBI! YOU CAN NOT WIN AGAINST ME!" **The fox stopped when it saw Naruto summon a great sword that was engulfed in flames. Naruto just stepped into the fox's cage. The fox was about to attack when it felt its head burning. The burning pain spread until the fox felt it everywhere.

"Kyuubi no Kitsune! My presence harms those born in the warp. If you give up now, I can send you back to the warp without any pain. Refuse me and you will be asking for death."

**"DIE!" **The fox swung its paw at Naruto. Naruto just raised his sword and slashed at it. The fox howled in pain and moved away from Naruto. **"I give up! Just one thing before I leave. How did you get so strong**,"the fox asked as Naruto unleashed a psychic blast.

"I AM THE ARCH-ENEMY OF THE CHAOS GODS! I WILL NOT DIE WHILE THEY EXIST! I AM THE GOD-EMPOROR OF MANKIND!" As the fox was taken back into the warp, Naruto's mindscape turned white. Naruto covered his psychic energy again and looked around. Then before his eyes, two people formed. The first was a woman. She had long red hair and was wearing a simple dress. The second person was man who had blond spiky hair. He had a white coat on with flames on the end. Both of them looked at Naruto with wide eyes. Naruto just smiled. "Hello mom and dad."

The red head started crying and hugging Naruto. The blond just smiled. "Naruto my baby boy! Look at you!" Naruto hugged the woman back.

"Hello Naruto. I wanted to see you, but the only time I could see you if the seal with the Kyuubi messed up," the blond man (Minato from now on) said.

"Dad, I sent the fox back to where it came from."

"WHAT? How," the red head (Kushina) asked with wide eyes.

"Mom and Dad get ready for a long story." Naruto began to tell his parents every thing. By the time he was done, his parents just stared at him. "And that's about it."

Kushina was the first one to speak, "OMG! MY SON BECOMES THE GOD EMPORER OF MANKIND! THAT IS SO COOL!" Minato and Naruto just shook their heads.

"Yeah, pretty cool huh? Oh dad I got something for you. I now how the 'death god' ate part of your soul. Normally, you would be stick with it forever. So, that is why I am taking your soul away from it." Minato was about to ask what his son was talking about when he felt something cold."

**"His soul is mine,"** a dark cold voice said. Naruto turned and saw a ghostly figure. The figure had no legs and was floating. It had a sword in its mouth. Besides that, Naruto could not make out anything.

"From this point on, Minato's soul is free. So go back to the shadows xeno!" Naruto raised his sword and unleashed part of his psychic energy. The figure (Shinigami) gasped at the power. "Release him now or die."

**"Take his soul. But just you wait; Kami and the others will want your head."** With that, the Shinigami was gone. Naruto turned around to his parents. Minato had tears of joy.

"Naruto, thank you. I can not thank you enough I-"

"I love you dad. Go free and be at peace." With that both of his parents faded away. But not before saying 'I love you son'. Naruto smiled and closed his eyes.

/ / / / / / / / Real World

Naruto opened his eyes and saw he was back in his apartment. He turned his head and looked at the clock. It was 9:45 A.M. _'Just enough time to get to the training ground,'_ the leader of mankind thought. After pulling on his orange jacket (Yes, he kept the orange jumpsuit. He really loves it!) He ran out the door. As he passed some of the villagers, he saw glares from them. _'If only they knew,' _he thought. When he arrived at the training grounds, he saw Sasuke and Sakura.

"Hi guys," he said as walked into the clearing.

"NARUTO! You stupid ninja-wanna be! Your late," Sakura yelled at the blond. Naruto ignored her. "Look at me when I'm talking to you!" Naruto turned to her and looked at her with cold eyes. When Sakura saw his eyes she stepped away. A few seconds later, Kakashi walked into the clearing.

"Yo," he said lazily. Sakura began to berate the copy-nin. He just ignored her. Kakashi pulled out two bells. "Ok team 7. Your goal is to get these two bells from within two hours."

"But sensei, there are only two bells," Sakura said confused.

"I know. One of you will not get one of the bells. The one who is without a bell well be sent back to the academy. You have two hours starting now!" Sasuke and Sakura jumped into the trees around the training field. Naruto just looked bored. Kakashi just looked at the blond with a raised eyebrow. "You know, you're kinda of weird." Naruto just reached into his pocket and pulled out a . . . book. Naruto opened the book and began to read it. "A book? You know this is a combat test, right?"

"Yep! But don't worry, I'm not worried about you," Naruto replied. Kakashi just looked at Naruto like he was crazy. Kakashi smirked under his mask. Kakashi in a blink of an eye went for a punch to Naruto's face. Naruto just blocked the punch like it was nothing and kept reading his book. Kakashi then sent a fury of kicks and punches towards Naruto. Much to Kakashi's shock, Naruto blocked and dodged every one. Naruto disappred and appeared behind Kakashi. Naruto had his hand crossed and two of his fingers together. "1000 years of death!" Kakashi eyes grew to the size of dinner plates as he felt pain. Kakashi shot into the air and landed into the river. Naruto just kept on reading. He stopped when he saw a little orange book. A large evil grin rested on Naruto's face.

/ / / / / / With Kakashi

_'I can't believe it! I was beaten by a genin! Not any genin, but the dead last one! I'll get that little brat later. I better test the other two,' _Kakashi thought. Kakashi jumped out of the water into a group of trees. Out of the corner of his eyes he could see Naruto still reading his book. Pushing Naruto out of his mind, Kakashi went in search of the other two.

/ / / / / / / / an Hour Later with Naruto

Naruto closed the book he was reading when he felt Kakashi come out of the tree line. He turned around and looked at Kakashi. "So, what did you do to the other two," he asked.

"Sasuke is busy digging himself out, and Sakura is having a nightmare. Now Naruto, you ready for round two?" Naruto just laughed and reached into his pocket. "Another book?"

"Yeah. A cat's copy of Icha Icha Paradise. Garbage if you ask me!" Naruto held up the orange book and opened it. Kakashi eyes widened when he heard his favorite book insulted. Then to Kakashi's horror, Naruto began to tear pages out of it. Kakashi yelled and charged at the blond with a kunai. Naruto smirked and dodged the kunai. He sent a quick sharp kick to Kakashi's head. Kakashi fell to the ground in pain. Naruto smirked and picked up the two bells. _'Maybe I over did it," _he thought while he opened his book again to read.

/ / / / / / another Hour Later

Naruto closed his book when he heard the timer go off. Kakashi groaned and stood up. Sasuke and Sakura walked out of the trees. Sasuke was covered in dirt, while Sakura was a little shaken up. Naruto looked at the two and smirked. Kakashi turned towards the three genin. "Well, since no one got a bell, you all have to go back now." Naruto held up two bells. Sasuke glared at the blond, while Sakura was about to go on a fan girl rant. "Well, Naruto it seems that you have an extra bell. What are you going to do with it?" Naruto smirked and threw both of the bells towards Sasuke and Sakura.

"Easy! Give them to my teammates! This test was about teamwork from the start." Sasuke and Sakura looked at the blond like he was stupid. Kakashi was beaming with happiness.

"Good job Naruto! He is right! This test was to test your teamwork. None of you, well I should say Sasuke and Sakura, could take me on without help from someone else. In the ninja world, those who break the rules are trash, that's true, but those who abandon their comrades are something worse then trash. From this point on, we are Team Seven. Meet me here tomorrow for the start of missions and training. You are dismissed! Oh and Naruto, we got to talk." Sasuke and Sakura walked back to the village. "Naruto, you are said to be the dead last of your class, but you fought me like I was nothing. To make it worse you even beat me. Tell me why the report and the truth are so different?"

"I've been holding my real skills back in fear of what the villagers would do to me if they knew my real power. Anyways I got to go talk to the old man!" Naruto turned around and went straight towards the Hokage tower. Kakashi just shook his head and walked back to the village when a thought hit him.

_'WHAT ABOUT MY ICHA ICHA? DAMN YOU NARUTO!'_

/ / / / / Hokage Tower with Naruto

Naruto walked up the stairs up towards the Hokage's office. Old women tried and stop him, but Naruto just slammed her head into her desk with his mind. When he reached the double doors he slammed the doors open. Sarutobi, the third hokage, was sitting behind his desk looking at some papers. He looked up and saw Naruto. He smiled warmly and said, "Hello Naruto. How can I help you today?"

"Cut the crap Sarutobi. When were you going to tell me about my parents? How about give me what was left for me," Naruto asked coldly. Sarutobi's eyes grew large.

"Naruto, I told you I do not kno-"

"I know every thing you kept from me! Do not lie to me."

"Fine then Naruto. How did you find out about your parents?"

"I meet them after the kyuubi died in the seal. It turns out that the seal was meant to kill the fox."

"Minato never told me much about the seal. Naruto, your parents left you a house and a large sum of money. The house is located in the woods near the hokage monument. Here is the key." Sarutobi opened his desk and took out a key. Naruto took it and left the office.

**Done for now. Vote and review!**


	3. Chapter 3

**Hello everyone and welcome to a new chapter! The Poll will come to an end next chapter, so VOTE! Other then that, no new news.**

**Oh this Disclaimer goes out to: ****Ektro234**

**Gondor20 owes nothing you read about in this story. It belongs to some heretic. For Russ and the All Father! **

**Uh, thanks Space Wolves.**

Chapter 2: The Return of the Caluthien and the search for Kami and the others

Naruto took a sip from his tea glass and turned the page in his book. He was currently sitting in the library of his parent's house. The house was good sized. It held many bedrooms, a large library, a cave system the ran under the house. The yard and garden were a mess, but he would get around to cleaning it up.

Naruto was about to turn the page when he heard a bang from the kitchen area down stairs. Naruto got up and grabbed a small pistol from the table next to him. He slowly walked down to the kitchen. He reached out with his mind and could feel a person in the room. In a few seconds, Naruto turned on the lights and grabbed the person by the neck. When Naruto focused, he saw the thin, pale face of Caluthien. Her eyes were wide with fear. Naruto blinked and let go of her. She fell to the ground, and just stared at him with fear. Naruto just sighed. _'Maybe I over did it. I'll give her a few minutes to get herself together,'_ Naruto thought as he pulled two tea begs from a cabinet. Three minutes later, Caluthien blinked and looked around. She saw she was on the floor. She looked up and saw a blond hair teen sipping tea. He wore orange robes.

Naruto looked at her and smiled. He nodded at the chair across from him. Caluthien slowly got up from the floor and sat in the chair. She looked down and saw a cup of tea. "So, what are you doing here Caluthien," Naruto asked. Caluthien looked shocked. "Oh! I get it. I am Naruto Uzumaki. You know me as 'The God Emperor of Mankind'."

"You can't be him! The Emperor had brown hair and was a little bit more tanner then you!"

"I have yet to change my hair color. Also, my skin will darken as time passes." Caluthien, being unsure, asked Naruto questions. Much to Caluthien's shock, Naruto got everyone of the questions right. "Ok, enough of the questions. What are you doing here?"

"Right. Let me explain. You see, when you were about to go back in time, I went into your room to check on you. You were about to finish these strange hand seals. When you did, there was a flash of light. When I came to, I was in the middle of a battlefield. Some humans saw me, and called me a bloodline whore. I killed them of course and fled. I was lost, but when I was sleeping one night, I felt your presence. I was able to follow it. I came upon this house and saw it. I was about to head up stairs, but you attacked me," Caluthien explained. Naruto just drank his tea. "By the way, I found this scroll." Caluthien put one of Naruto's sealing scrolls on the table. "It has your hand writing on it."

Naruto smiled and took the scroll. He unsealed the first item. Out came a large golden boot. Naruto eyes grew large. "MY ARMOR! HELL YEAH! KICK ASS! WITH THIS, I'LL KICK ASS AND CHEW BUBBLEGUM. . . AND I'M ALL OUT OF GUM!" Naruto began to unseal different parts of his armor. Naruto closed his eyes, and in a bright light stood the Emperor Caluthien remembered. Caluthien just watched as Naruto jumped around the room yelling like an Ork on his first WAAAGH. Naruto stopped and turned to her. "As for you. You can stay in one of the bedrooms. It seems you are stuck here with me! I will fill you in on everything in the morning! I got to go mess with my armor." Naruto went up and hug the Eldar far seer. "Thanks for getting this for me. I'll talk to you in the morning." Naruto left the room not noticing a large blush on Caluthien's face.

/ / / / / / / / Next Morning

Naruto sat at his kitchen table in his orange jumpsuit eating ramen. He had spent most of the night working on a new type of armor. This armor was going to be faster, lighter, and tougher then the pervious one. Naruto looked up when he heard foot steps coming towards the kitchen. Caluthien walked in wearing a purple dress. Her blond hair was in a bun. She looked at Naruto and looks away.

"What are you wearing," she asks.

"One of my favorite outfits of all time!" Caluthien looks at Naruto like he was crazy. "Anyways, I got some things to do today. I got to go to a team meeting. If you want to go out, cover up your ears."

"Team meeting," Caluthien asked confused. Naruto nodded and began to explain about the ninja system, the Kyuubi, and a few other things about his life. "Wait. You're the most powerful person alive. You don't need to train."

"That's the thing. I don't YET have all my powers back. It will take a while for me to be at full strength. When I went back in time it took a lot of power. There are some things that are nearly impossible. Bending space and time is one of them. To make things worse, others jumped on with me."

"What do you mean?"

"When I went back in time, I felt others. I felt four dark powers with me. You know of whom I speak of."

"The Chaos Gods?"

"Yes. They came back with me. As you know, this is very bad. We could be dealing with demons in a few years. Add this to Kami and the others; we have a lot of work to do."

"Can you tell where the Chaos Gods and Kami are? You should be able to pick their location up."

"As I said, my powers are not at full yet. It will take a while for them to re-charge."

"How long?"

"For them to all return, about five years."

"What if Chaos moves before then?"

"I may not be at full power, but I still can take on any demons that come my way. As for Kami and the others, I can't say. I don't even know what they are. I have a few ideas though."

"What are you thinking?"

"I have four ideas. One, they are C'tan. There are a few issues with this idea. Such as no necrons. Two, a type of Pre-Chaos demons. Three, a type of alien. Four, a spirit of something." Naruto and Caluthien just sat there. "Caluthien, if you want to help me, go to the library and read up on any thing about Kami and the other 'Gods'. Take notes too. I got to go, so talk to you later." Naruto smiled and walked out of the kitchen.

/ / / / / / / / / At the Library with Caluthien

Caluthien sat down a group of books on a table and took a seat. She picked the first one up and opened it. (Note: Books and notes will be in bold italics like _**this**_.)

_** Kami sent her grand angles into battle against the wicked men! The wicked men could not damage Kami's metal angles! Shinigami devoured the souls of the wicked men. **_

_"This sounds like the C'tan, but they would devour the entire planet, not leave people alive,_" Caluthien thought as she read some more. A few hours later, the Eldar had no answers. _"There are so many gods! I don't think there was so many C'tan, but those angles are very similar to the necrons." _

_/ / / / / / / / _**Some** Island near Wave

Iwao was a simple farmer. He had a wife and three kids. He sighed as he pushed his cart across his field. He was thinking about his fun time with his wife last night when he felt his cart hit something. He looked down and saw a large black book with a golden eight pointed star. Iwao opened the book up and began to read. A few minutes later, he closed the book. _"These Chaos Gods don't sound to bad. Maybe a prayer to one won't hurt." _

/ / / / / / / / / / A Sound Ninja base

Orochimaru looked at the strange book on his desk. It had a strange blue symbol. He opened it and began to read. As he read the book, he smiled. Knowledge, power, magic. _"Ku ku ku ku. This Tzeentch sounds like a good god._

_/ / / / / _ The Hidden Sand Village

Gaara smirked as he killed a villager who tried and kill him. His 'Mothers' voice is gone. He was a slave to her no longer. He had a god to fight and spill for. Gaara turned and saw a villager attack. "Blood for the Blood God, Skull for the Skull Throne," Gaara yelled as he killed the man.

/ / / / / / A Hot Spring in Fire Country

Jiraiya's nose began to bleed as he watched a woman wash herself. He leaned forward and fell out of the tree. He groaned as he got up. Out of the corner of his eye, he saw a book with a strange pink symbol. He picked the book up and began to read. _"A god of Pervasion? COUNT ME IN! ALL HAIL SLAANESH!"_

/ / / / / / / / Konoha

Choza Akimichi smiled as he watched his son train. His clan was becoming strong. He himself was learning something new. This morning, he found on his desk a book. It talked about a god called Nurgle. As he read it, this god was good. He was of Joy and death. He disliked the death part, but he learned that it was important. Tonight he was going to pray and ask for a disease to help his clan. _"I know Papa Nurgle will help the Akimichi!_".

**Done. Sorry for the delay, but I just got Dawn of War 2. It is a Fun game. I got it on steam with the expansions packs for 60 bucks. Also, I have changed the paring. Naruto will only be with Caluthien. If you want another pairing to show up, leave it in the review. Thanks, and see you next time.**


	4. Chapter 4

**Hello, and welcome to a new chapter! I know I just updated, but I have a lot of ideas to write down. As for those who turned to the Chaos Gods, I had an easy time picking them out until I got to Nurgle. I had a hard time finding a good match. I was thinking Shino, but Nurgle is known for joy.**

**Anyways on to the story.**

**Disclamer: Gondor20, for the Greater God, does not own anything found in the story. It belongs to someone else.**

**Uh, thanks Tau.**

Chapter 3: Chaos Rising and The Holy Orders of the Emperor's Inquisition

Naruto smiled as he finished his sniper rifle. While he would normally use his sword, he needed a weapon for stealth and for ninja work. It had been four months since Caluthien arrived and things have been quiet. He had no leads on Chaos or Kami. _'The Chaos Gods are never this quiet. They must be planning something.'_ Naruto thought with a frown. The rule he learned with the Chaos Gods was when they are quiet, they are planning something. He came to learn that with the Great Crusade. The Chaos Gods made no move, and then suddenly Horus turned.

Naruto looked up when he saw Caluthien walk into his lab. The two become friends before he went back in time, but the friendship grew even more now. Nothing romantic. "Any new leads on Kami," Naruto asked. Caluthien sighed.

"None. Four months of research, and no leads. I don't even know what the hell they even are," Caluthien replied. Naruto learned one major thing about the Eldar farseer. She hated being wrong and not understanding something.

"I guess we'll have to wait until they reveal themselves. Until then-" Naruto closed his eyes. He stayed this way for a few minutes. He opened his eyes. "A portal to the wrap has opened. I can feel it."

"Where?"

"An island near Wave. I was able to make out a village." Naruto closed his eyes again. A few seconds later, he opened his eyes. "It's gone now, but still we need to check it out. Pack our stuff for a trip. I got a team meeting to go to."

/ / / / / / / / / / / / / Hokage Office

Sarutobi looked at the three jounin in front of him. "I have called you here for an A-ranked mission to an island near Wave Country. Two weeks ago, wagons going to the village of Kuro have been missing. A merchant guild has sent an armed escort with the last one. Only one of the guards came back. He talked about how the villagers tried to kill him. He kept talking about how the land seemed changed. Kakashi, Asuma, and Kurenai, you three are to find out what has been going on. Pack for a standard A-rank mission. You leave tomorrow morning. Dismissed." The jounin bowed and left the room.

/ / / / / / / / Team 7 Training Ground

Naruto watched the clouds passed as he waited for Kakashi to show up. He turned his teammates. Sakura was being a fan girl and looked like she was going to rape Sasuke. Sasuke was . . . brooding. _'What a normal day for team 7,'_ Naruto thought with a chuckle.

"What's so funny ninja wanna be," Sakura yelled. Naruto just laughed and closed his eyes.

"Tell me Sakura. How many jutsu do you know? Oh, and what are there ranks?" Sakura's face grew red. She was about to yell at Naruto when Kakashi walked out of the bushes. Naruto stood up and yawned.

"Hello team. I've got some bad news. I have an A-ranked mission I must go on with some of the other senseis. You have till I come back to rest and do some solo training! Have fun!" Kakashi began to walk away, not even caring about his teams response. Naruto shrugged and began to walk home. Sakura turned and was about to yell at Naruto, but found him gone.

/ / / / / / / / / Later That Night

Naruto and Caluthien walked along the road towards Wave. They had left in the evening. Naruto was wearing black body armor. Caluthien was wearing an all black version of her far seer armor without the helmet. Naruto turned to Caluthien. "Let's camp for the night. As we draw closer to Wave, I want to be more rested incase we ran into anything." Caluthien nodded and they broke off into the forest near the road.

Thirty minutes later, Naruto and Caluthien sat around a fire eating a meal out of a can. Neither said anything to the other, until Caluthien spoke. "What do you think we'll find?"

"Can't say I know. Could be nothing. A ninja working on a jutsu maybe. Or a demon entering this realm that is going to kill us." Silence once again reigns at the fire.

"Naruto, I know this is a strange question, but I'm curious," Caluthien said. Naruto nodded. "Did you ever have a wife or kids?"

Naruto did not speak. Caluthien was about to apologies, but Naruto spoke. "I had a wife. No kids."

"Who was she?"

"Her name was Hinata Hyuuga."

"That girl who followed you?"

"Yes." Naruto sighed and closed his eyes. "I left her." Caluthien eyes widened. "I became Hokage of Konoha. There were nights I could not spend at home with her. She had needs, if you catch my drift. Her teammate, Kiba, helped her. I came home one night to surprise her, and found Kiba on her. I kicked her out and burned the bed. The two then had a child and lived happily." Naruto got up and walked towards his tent. "Good night Caluthien."

Caluthien looked into the fire a little bit longer. _'I don't think anyone has ever seen this side of the Emperor. I would never think his life was so sad. So much betrayal. That boy named Sasuke, his brother. Hinata, his wife. Horus, his son.'_

/ / / / / A few Days later near the Village

Naruto and Caluthien looked at the warped tree. The once green leaves are now blood red. The bark, once brown, is now a bone white. Burnt into the tree was a black, eight pointed star. "The mark of Chaos as clear as day," Naruto said. Naruto had his sniper rifle in his hands. "Caluthien. Spilt up and go around the village." Naruto handed a small ear bud. "We'll use this to talk to each other." Caluthien nodded and walked away. Naruto put the ear bud in, and walked into the woods.

For half an hour, Naruto would only find warped tree or plants. Naruto sighed and walked through a large group of bushes. He saw on the other side, a small brick home. Naruto raised his rifle and looked around. Nothing. With his rifle still raised, Naruto moved forward looking for any movement. He reached the door to the home. He kicked it opened. The smell of blood hit him hard. He looked in and could not help but to cringe. Inside was the body of a naked woman. Her insides were laid around her and formed the Chaos star.

"DIE! IN THE NAME OF THE CHAOS GODS," a voice yelled. Naruto quickly shot his rifle in the direction. A sick sound was made and then a thump. Naruto moved towards the body. It was a man. The man was lying in a pool of blood. The man was about middle aged and wore all white. A large red flower was growing on the man's chest. "YOU CAN"T BEAT ME! I AM A FOLLOWER OF THE DARK APOSTLE IWAO!" Naruto shot the man in the head.

"Caluthien, I've found something," Naruto said. "I found a house with a body in it. A man then attacks me, talking about a guy named Iwao. How about you? You find anything?"

"Just warped trees. It's strange. I hear no birds," Naruto heard Caluthien say. Naruto listened. He heard nothing.

"Your right. Contact me if you need me." Naruto turned and walked back into the forest.

/ / / / / An Hour Later

Naruto walked into a clearing and saw Caluthien waiting for him. "Anything?" Caluthien moved to the side and Naruto saw a bear. The bear had little hair and had burn and slash marks all over it. On its face was the symbol of the Blood God.

"The Warp energy is destroying the animals that have not fled. This bear, a mother bear, killed its cubs. Naruto, I have never seen a mother kill its children. It is unheard of," Caluthien said with a serious tone.

"That bad. Let's move into the village and see if we can find anything. Be on guard." Naruto and Caluthien began to walk towards the village.

/ / / / / In the Village

Naruto walked along the street towards the center of the village. He saw the bodies of men, women, and children along the road. Some of the buildings were on fire. Caluthien had her spear out and was focusing energy into her hand incase of an attack. "What a blood bath," Naruto mumbled. Naruto felt something watching to the left of him. "Spider stalking noble." Caluthien nodded and glanced towards the ruins of a building. Within a blink of an eye, lightening shot from her hands. Naruto heard three screams. With his rifle raised, Naruto ran to the building. Lying on the ground was two men and a woman. "Kakashi? Asuma? Kurenai? What the hell are you doing here?"

"Naruto? What the hell are YOU doing here? I doubt the Hokage sent you. Also, who are you with," Kakashi asked with a glare.

"It's a long story," Naruto said as he helped the three jounin. "You guys should leave as fast as possible."

"You're nothing but a genin! You should not be out of the village. You are to come with us. Wait till Lord Hokage hea-", Kakashi was cut off by Caluthien.

"NARUTO! WE GOT COMPANY!" Naruto ran from the three jounin and saw a mob of villagers. They had different weapons, such as pitchforks. Naruto kneeled and began to fire at the mob. Caluthien was firing off blots of fire from her hands.

"Kakashi, stop standing around and help!" Kakashi jumped from the ruins and sent a volley of kunai towards the crowd. Asuma jumped out and landed next to Naruto. He pulled his knives out and got ready.

Some of the villagers began to attack each other as Kurenai cast a genjutsu on some of them. When the mob was close, Asuma rushed forward and began to cut his way through the mob. Caluthien soon followed with her spear and began to fight. Naruto pulled his power sword and was about to attack when he sensed something. He ducked and looked up and saw a blood letter with a flaming sword. Naruto brought his sword up and blocked another strike. He focused energy into his blade and lashed out killing the demon. Naruto turned and attacked the nearest villager.

"CHIDORI!" Naruto saw out of the corner of his eye and saw Kakashi cutting threw a group of villagers.

Naruto cut down the last of the villagers. He looked and saw the Chaos star on their forehead. "What the hell happened to them," Naruto heard Kurenai said.

"Caluthien! Towards the center of the Village," Naruto said running down the street. Caluthien ran after him.

"Naruto! Wait," Kakashi yelled. The three jounin rushed after him. When the reached him, they could not help to be sick. In the middle of the village was an alter made out of bodies. Kurenai began to get sick looking at it. Kakashi saw a look of pure rage of Naruto's face.

"Caluthien, search the bodies for anything about this Iwao." Caluthien nodded.

"Wait! Iwao? He was the same one the Merchant Guild talked about. He asked for the goods," Asuma said stepping forward.

"A trap. He lured them to their deaths," Naruto said darkly.

"Naruto! What the hell is going on," Kakashi yelled.

"Kakashi. We all need to head back to Konoha. I need to talk to the Hokage about this," Naruto said.

"Naruto. I found a letter. It said Iwao has left the islands to spread the word," Caluthien said giving Naruto the letter. Naruto was about to say something when he saw a red dot on Caluthien's forehead. He pushed her down as a loud boom was heard. Naruto drew his pistol shot at the source. After a few seconds, Naruto ran towards the building. He saw a sniper rifle laying down. He picked it up and looked at it.

The sniper rifle was made out of metal. It was in very good condition. Naruto knew who would have this weapon. A Space Marine Chapter. Naruto walked over to Caluthien. "A sniper rifle. Space Marine scout issued." Caluthien eyes grew. "We are not alone here."

"Is there a serial number on it," she asked.

"It would be in the gun. We'll have to wait till we get back to Konoha to open it. Even still, I can tell this has been used. The number may be gone due to use. We need to get back to Konoha as quick in possible." Naruto and Caluthien began to walk away. "Kakashi, you coming?"

/ / / / / / / / Konoha: A few days later

Naruto, Caluthien, and the jounin walked into the Hokage's office. Sarutobi looked up and was shocked to see Naruto and a strange looking woman. "Naruto, what are you doing here?"

"Sarutobi, we have a lot to talk about. I think you need to know some things. Important things." Naruto then began to tell his tale. By the end of it, Asuma, Kakashi, Sarutobi, and Kurenai had their mouths hanging open. The room was silent for a long time. Naruto was leaning against the wall with his bangs over his eyes.

"Naruto, I see no lies in your eyes. I believe you. What can you tell me about Chaos," Sarutobi asked grimly.

"Chaos is hard to describe. The main followers of Chaos are demons. They live in a realm called the Warp. They use humans in this realm to do their work. Sometimes, demons can come to this realm, but not for long. This enemy is unlike anything you would had deal with in the past."

"How do we fight it and win?"

"You don't fight it. I will, along with Caluthien. This war must be in secret till the right time. I will need help."

"Ok, Naruto. What do you need?"

"I need eyes and ears. Agents who will fight Chaos when I can't. I am planning to remake the Inquisition and the Grey Knights. They shall be the weapons of mankind against the forces of Chaos and darkness. They shall know no fear." Everyone in the room felt hope and light. "I will need people. They must be strong. I must wait on making the Grey Knights, but I can make the Inquisition."

"I will allow you to recruit any Konoha ninja you want for the Inquisition. Any ideas yet?"

"I have a few. I'm thinking about Asuma Sarutobi." Asuma looked up with wide eyes.

"Why me," he asked.

"You are strong and smart. You have honor and morals."

"What about my team?"

"I will have someone else train them," Sarutobi said looking at a piece of paper.

"So, Asuma, are you in," Naruto said holding out his hand. Asuma did not speak for a long time. He then shook Naruto's hand and then kneeled.

"I, Asuma Sarutobi, give you my life and service. I shall be your weapon, my Emperor."

"Rise, Asuma. Go home and rest. In two days time, come to my home and we shall began training."

"You are all dismissed! Also, this is an SS-rank secret. No one shall speak of this," the Hokage said. "Oh, and Naruto. Will you still be with your team?"

"Yes for now. I may have to send a clone sometimes. I will help Konoha for their service."

/ / / / / / /

Caluthien smiled as Naruto held her in his arms. He rubbed a large bulge that was her stomach. He kissed her. "I love you, Caluthien," Naruto said.

/ / / /

Caluthien blocked another hit. She looked up and saw Naruto, clad in his golden armor, fighting a large demon.

/ / / / / / Konoha

Caluthien woke up with sweat on her face. She looked at the clock near her bed and saw it was only 3am. _'Dreams. Just dreams. Or visions,'_ Caluthien lay back down and went into a dreamless sleep.

**This is the end of this chapter. Sorry for any spelling mistakes. No flames. **


	5. Chapter 5

**Important! Read Below: **

**Hello readers. Every once in a while, I will make a side story/ filler chapter that will go into depth about different things. I will space these chapters out, so don't worry about reading eight filler chapters in a row. I highly recommend reading them, because it will give you incite into Naruto's history. These chapters will not typically be very long. This will be in Naruto's P.O.V first person.**

**Disclaimer: I don't own anything.**

**Also, check out my other warhammer story. That one is a happier yet funny and gruesome story.**

I smiled as I walked out of the Hokage's office. It had been a very long day. In the morning, I had a meeting with some clan heads. They told me about what has been going on in their clans. After the meeting, I had a large stack of paperwork to do till noon. At noon, I went to lunch with Kakashi-sensei and his wife, Shizune. I was extremely shocked when I heard about those two getting married. It felt nice talking with Kakashi and Shizune. When I was appointed Hokage, I saw my friends less. Anyways, we talked about everything, ranging from Tsunade's bad luck to Kakashi being a father. I still can picture it. Kakashi and a little boy both reading Icha Icha and Shizune getting pissed.

After lunch, I had a meeting with the Kumo diplomat. The meeting consisted of him telling why I should arrange a marriage between a Hyuuga and a Kumo ninja. I kindly declined the offer, but said I would think about it in the future, a total lie by the way. I hate arranged marriages. It lowers the power of love in my mind. After that meeting, I finished my paperwork from the morning. Thanks to shadow clones, I was able to get it done very early and was able to go home to Hinata, my wife.

Hinata confessed her love for me during Pein's attack on Konoha. For the longest time, I forgot about it due to the war and other things. After the fourth great shinobi war, I asked Hinata out on a date and we went from there. A year later, I asked her to be my wife. She accepted without a heartbeat. The wedding was one of the largest the Elemental Nations had ever seen. People from all over came to see it. An old looking Tsunade married us. We spent our honeymoon making love in a cabin in the middle of the woods. Our marriage was perfect . . . too perfect.

As I was saying, I was walking home. Our home was small, but nice. I opened the front door and called for Hinata. She did not respond. This was not uncommon. She was out of the house or sleeping. I walked up towards our bedroom and began to hear strange sounds. I opened the bedroom door and gasped. There I saw Hinata, my wife, bent over in front of Kiba Inuzuka, clan heir for the Inuzuka, taking it from behind. I just starred. Hinata looked over and grew pale. I closed the door and went to the kitchen. I do not know how long I sat there, but soon Kiba and Hinata came in, both dressed.

"Naruto-kun. I'm so sorry," Hinata said in a small voice. She began to push her fingers together. It was something she did when she was stressed. I looked up at them with tears rolling down my face.

"How long," I asked.

"A year ago," Kiba replied sheepishly rubbing the back of his head. We were already married for two months when they started. I balled my fist.

"I want both of you to get out of this house now," I said in a low whisper, with tears rolling down my face.

"Naruto-kun-"

"Don't use -kun! You lost that right! Get out now," I yelled. Both Kiba and Hinata ran out of the house. I just sat there for hours. I was broken out of my shock when I heard a knock at the door. I got up and answered it. Sasuke and Sakura stood their with concerned looks on their face.

"Naruto! I heard about what happened. I'm so sorry," Sakura said hugging me. I did not return the hug. Sakura pulled back and smiled sadly. "Naruto, we are here for you. Your friends are all here for you."

I turned around. "I don't need anyone. I can fend for myself," I replied. Sakura was shocked and was about to say something until Sasuke spoke up.

"Ok Naruto. Remember, we are here for you. When you're ready to talk about it, we will listen." Sasuke closed the door. I walked to the bedroom. I could still smell it! I closed the door and went to sleep on the coach. The vision I had would change the galaxy.

I awoke to find myself in a hellish landscape. I could here screams and see monsters that no nightmare could create. I looked up and saw three small balls. The first ball was red. I felt anger and war from it. The next ball was blue. I felt schemes and hidden meanings. The last ball was a sickly green colored. I felt death and decay. I would come to learn that these three balls were the start of the first three Chaos Gods, Khorne, Tzeentch, and Nurgle. Slaanesh would be formed later during the fall of the Eldar. This started my path towards bringing peace to all and my path to God-Emperor of Mankind.

For the next two weeks, I did my duties of Hokage. At night, I would drink and eat ramen, hoping for some pleasure. I did not use the bedroom anymore, even after Sasuke destroyed the bed with a fire Jutsu. Hinata sent a branch member to collect her things.

One day, as I was sitting in the Hokage's office, Hinata and Kiba showed up.

"Lord Hokage. I wish to wed Hinata Hyuuga," Kiba said with fear in his voice. In Konoha, only one person has the power to marry ninja, and that is the Hokage.

"What are your reasons," I asked in a mono-toned voice.

"She is pregnant with our child and I love her," he said. I sighed.

"I understand. Tell Shizune the date of the wedding, and I will be there," I said with a large frown. "Now, please leave my office. I have much work to do." They both left. Once they were gone, I cried some more. I could still not believe it.

Two months later, I stood in front of church in my hokage robes. The hat covered my face. Kiba was looking nervous. I saw Sakura look sadly at me. Soon, Hinata came down the aisle in a white gown. A large bump replaced her stomach. I did the wedding as a Hokage should and then quickly left. That night, as I was finishing my tenth bottle of sake, I felt some strange. I could feel energy around me. I could feel the hellish landscape, but it was not there. I could feel the galaxy all around me. I soon passed out, but in the morning I thought hard on the subject. The hellish landscape I called 'The Immaterium' or 'The Warp'. As for the feelings, I would mediate more on them. I came to the conclusion, that the abilities were not charka based or a bloodline. They were something different. I would mediate and draw the energy out. I soon dubbed the powers as 'psychic powers' and so I became a psyker.


	6. Chapter 6

Hello. This is gondor201. It's been a very long time. I can't really say sorry enough for not updating my stories. I have been working on my own personal writings (non-fan fiction) and that's my reason. I will be deleting my stories, but there's more.

I will be making a new account: Kugelblitz. I will be working on more Naruto fan fiction (maybe no crossovers yet). Again sorry for not updating.

My first (new story) will be uploaded sometime this week before Friday (maybe today, but no promises).


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